# 27-2-2020 JHZ

function initialize()
{

  export Caprion=$INF/Caprion
  export interval=/rds/project/jmmh2/rds-jmmh2-post_qc_data/interval/imputed/uk10k_1000g_b37/imputed

  sed 's/ID_1/FID/;s/ID_2/IID/' swath-ms.sample > swath-ms-bolt.sample
  plink --bfile merged_imputation --remove affymetrix.id2 --make-bed --out swath-ms

  sed '1,2d' swath-ms.sample | cut -d' ' -f1-2,4-26 > swath-ms.covar
  sed '2d' swath-ms.sample | cut -d' ' -f1-2,27-1244 | sed 's/ID_1/FID/;s/ID_2/IID/;s/NA/-9/g' > swath-ms.pheno
  paste  affymetrix.id affymetrix.id -d ' ' > swath-ms.id

}

function pgwas_bolt()
{
  export col=$(cut -d' ' -f $i swath-ms.uniprot)
  bolt \
      --bfile=swath-ms \
      --bgenFile=swath-ms-{1:22}.bgen \
      --bgenMinMAF=1e-2 \
      --bgenMinINFO=0.3 \
      --sampleFile=swath-ms.sample \
      --phenoFile=swath-ms-bolt.sample \
      --phenoCol=$col \
      --covarFile=swath-ms-bolt.sample \
      --covarCol=sex \
      --qCovarCol=age \
      --qCovarCol=bmi \
      --qCovarCol=PC{1:20} \
      --lmm \
      --LDscoresUseChip \
      --noMapCheck \
      --numLeaveOutChunks 2 \
      --statsFileBgenSnps=${col}.bgen-stats \
      --statsFile=${col}.stats \
      2>&1 | tee ${col}-bolt.log
  bolt \
      --bfile=swath-ms \
      --bgenFile=swath-ms-{1:22}.bgen \
      --bgenMinMAF=1e-2 \
      --bgenMinINFO=0.3 \
      --sampleFile=swath-ms.sample \
      --phenoFile=swath-ms-bolt.sample \
      --phenoCol=${col}_invn \
      --covarFile=swath-ms-bolt.sample \
      --covarCol=sex \
      --qCovarCol=age \
      --qCovarCol=bmi \
      --qCovarCol=PC{1:20} \
      --lmm \
      --LDscoresUseChip \
      --noMapCheck \
      --numLeaveOutChunks 2 \
      --statsFileBgenSnps=${col}_invn.bgen-stats \
      --statsFile=${col}.stats \
      2>&1 | tee ${col}_invn-bolt.log
}

function pgwas_snptest()
{
  export col=$(cut -d' ' -f $i swath-ms.uniprot)
  for i in $(seq 1 22)
  do
      snptest \
             -data swath-ms-${i}.bgen swath-ms.sample -log ${col}-snptest.log -cov_all \
             -filetype bgen \
             -frequentist 1 -hwe -missing_code NA,-999 -use_raw_covariates -use_raw_phenotypes \
             -method score \
             -pheno ${col} \
             -o ${col}-${i}.out
      snptest \
             -data swath-ms-${i}.bgen swath-ms.sample -log ${col}_invn-snptest.log -cov_all \
             -filetype bgen \
             -frequentist 1 -hwe -missing_code NA,-999 -use_raw_covariates -use_raw_phenotypes \
             -method score \
             -pheno ${col}_invn \
             -o ${col}_invn-${i}.out
  done
}

module load plink/2.00-alpha

function pgwas_plink2()
{
  export col=$(cut -d' ' -f $i swath-ms.uniprot)
  for i in $(seq 1 22)
  do
      plink2 \
             --bgen swath-ms-${i}.bgen --sample swath-ms.sample \
             --glm hide-covar --input-missing-phenotype -9 --covar-variance-standardize \
             --pheno swath-ms.pheno --pheno-name ${col} --covar swath-ms.covar \
             -out ${col}-${i}
      plink2 \
             --bgen swath-ms-${i}.bgen --sample swath-ms.sample \
             --glm hide-covar --input-missing-phenotype -9 --covar-variance-standardize \
             --pheno swath-ms.pheno --pheno-name ${col}_invn --covar swath-ms.covar \
             --out ${col}_invn-${i}
  done
}

function pgwas_quicktest()
{
  export col=$(cut -d' ' -f $i swath-ms.uniprot)
  for i in $(seq 1 22)
  do
      quicktest --geno swath-ms-${i}.bgen --pheno swath-ms.sample --snptest --bgen \
                --npheno ${col} --ncovar bmi --ncovar sex --ncovar age \
                --ncovar PC1 --ncovar PC2 --ncovar PC3 --ncovar PC4 --ncovar PC5  \
                --ncovar PC6 --ncovar PC7 --ncovar PC8 --ncovar PC9 --ncovar PC10 \
                --method-mean --method-score --compute-rSqHat --out ${col}-qt-${i}.out
  done
}